Overview

The data set used in this report was accessed from Columbia River DART and includes counts of adult fish passages through the Willamette Falls fish ladder between January 1, 2001 and December 31, 2010. This report is concerned with three species in particular: Coho Salmon (Oncorhynchus kisutch), Jack (young) Coho salmon (Oncorhynchus kisutch) and Steelhead Trout (Oncorhynchus mykiss). The results of the report are displayed as a time series plot, season plot, and total annual counts of adult fish passages through Willamette Falls by species.

Figure 1. Map and photo of Willamette Falls Fish Ladder in Orgeon City, Oregon. Every year thousands of fish, including threatened Lower Columbia River Coho Salmon and Steelhead, traverse up and down the fish ladder to travel to and from the sea to complete their life cycle.

Citations

Columbia Basin Research (2021). Data Courtesy of U.S. Army Corps of Engineers, NWD and Chelan, Douglas, and Grant County PUDs, Yakima Klickitat Fisheries Project, Colville Tribes Fish & Wildlife (OBMEP), Oregon Department of Fish & Wildlife, Washington Department of Fish & Wildlife. DART Adult Passage 1-1-2001 to 12-31-2010[data file]. Retrieved from http://www.cbr.washington.edu/dart/query/adult_graph_text

US Army Corps of Engineers. Portland District Website [image]. Retrieved from https://www.nwp.usace.army.mil/willamette/locks/

full_fish <- read_csv(here("data", "willamette_fish_passage.csv"))

Time Series

# Data wrangling
fish <- full_fish %>% 
  select("Project", "Date", "Steelhead","Coho","Jack Coho") %>% 
  clean_names() %>% 
  pivot_longer(
    cols = steelhead:jack_coho,
    names_to = "species",
    values_to = "count") %>% 
  mutate(count = replace_na(count, 0))

fish_ts <- fish %>% 
  mutate(date = lubridate::mdy(date)) %>% 
  as_tsibble(key = species, index = date)


# Time series graph
fish_ts1 <- fish %>% 
  mutate(date = lubridate::mdy(date)) %>% 
  as_tsibble(key = species, index = date) %>% 
  mutate(species = case_when(
    species == "coho" ~ "Coho",
    species == "jack_coho" ~ "Jack Coho",
    species == "steelhead" ~ "Steelhead"))
  
timeplot <- ggplot(data = fish_ts1, aes(x = date, y = count, color = species)) +
  geom_line(show.legend = FALSE) +
  facet_wrap( ~ species, dir = "v") +
  scale_color_manual(values = palette_grp) +
  theme_gray() +
  labs(x = "Year",
       y = "Fish Observations") +
  theme(plot.title = element_text(size = 14,
                                  face = "bold",
                                  hjust = 0.5),
        axis.title.y = element_text(size = 14),
        axis.title.x = element_text(size = 14))
  
  timeplot
**Figure 2.** Coho Salmon, Jack Coho Salmon, and Steelhead annual passage trends from January 1, 2001 to December 31, 2010 through the Willamette Fish Ladder.

Figure 2. Coho Salmon, Jack Coho Salmon, and Steelhead annual passage trends from January 1, 2001 to December 31, 2010 through the Willamette Fish Ladder.

Analysis:

  • Fish passage through Willamette Falls fish ladder displays seasonality for all three species but seasonal peaks differ between Steelhead and the Coho salmon
  • Fish passage through the fish ladder displays cyclicality for Coho and Jack Coho Salmon over period of 2 to 4 years
  • Adult Coho salmon passage through the fish ladder displays an overall positive trend from 2007 to 2010

Seasonplots

#trying to out a ggseason just to explore
fish_ts_season <- fish_ts

#steelhead only
steel <- fish_ts_season %>% 
  filter(species == "steelhead")

#color palette for steelhead
coul_steel <- brewer.pal(5, "Reds")
coul_steel <- colorRampPalette(coul_steel)(10)

#ggseason for steelhead
steel_plot <- 
  gg_season(data = steel, y = count, pal = coul_steel, show.legend = FALSE) +
  theme_gray() +
  labs(x = "Month",
       y = "", 
       title = "Steelhead") +
  theme(plot.title = element_text(size = 14,
                                   face = "bold",
        hjust = 0.5),
        axis.title.x = element_text(size = 14))


#coho only
coho <- fish_ts_season %>% 
  filter(species == "coho") 

#coho season plot
coho_plot <- 
  gg_season(data = coho, y = count, pal = pal_seegruen, show.legend = FALSE) +
  theme_gray() +
  labs(x = "",
       y = "", 
       title = "Coho") +
  theme(plot.title = element_text(size = 14,
                                   face = "bold",
        hjust = 0.5))



#jack coho only
jack_coho <- fish_ts_season %>% 
  filter(species == "jack_coho") 

#jack coho color palette
coul_jack <- brewer.pal(4, "Oranges")
coul_jack <- colorRampPalette(coul_jack)(10)

#jack coho season plot
jack_coho_plot <- 
  gg_season(data = jack_coho, y = count, pal = coul_jack, show.legend = FALSE) +
  theme_gray() +
  labs(x = "",
       y = "Fish Observations", 
       title = "Jack Coho") +
  theme(plot.title = element_text(size = 14,
                                   face = "bold",
        hjust = 0.5),
        axis.title.y = element_text(size = 14)) 


#put all 3 season plots together in 1 graph
season <- coho_plot/jack_coho_plot/steel_plot


season
**Figure 3.** Seasonal distribution of Coho Salmon, Jack Coho Salmon, and Steelhead observations at the Willamette Fish Ladder from 2001 to 2010.

Figure 3. Seasonal distribution of Coho Salmon, Jack Coho Salmon, and Steelhead observations at the Willamette Fish Ladder from 2001 to 2010.

Analysis:

  • Coho and Jack Coho peak seasonally in early October, with Jack Coho having the most centralized observations
  • Coho salmon observations have increased since 2001 and have the highest number of observations in a particular month
  • Steelhead salmon have the longest period of observation, ranging from January to August, peaking in June

Summary Statistics & Analysis

fish_index <- fish_ts1 %>% 
  index_by(year = ~ year(.)) %>% 
  group_by(species) %>% 
  summarise(total = sum(count)) 

fish_annual <- ggplot(data = fish_index, aes(x = year, y = total)) +
  geom_col(stat = identity, 
           aes(fill = species),
           show.legend = FALSE) +
  facet_wrap(~ species,
             dir = "v",
             scales = "free_y") +
  scale_x_continuous(n.breaks = 10) +
  scale_fill_manual(values = palette_grp) +
  labs(x = "Year",
       y = "Total Number of Fish") +
  theme_gray()

plotly::ggplotly(fish_annual) %>% 
  layout(showlegend = FALSE)

Figure 4. Total annual passage count of adult Coho Salmon, Jack Coho Salmon, and Stealhead Trout observed at Willamette Falls from the beginning of 2001 through the end of 2010. The scales of the y-axes are different for each species to render the data easier to visualize. Hover over a column to see the number of adult fish of that species observed for that year.

Analysis:

  • Jack Coho Salmon were the least commonly observed fish overall, and had a dramatic increase in numbers (over a fifteen-fold increase from 2007 to 2008) in the last three years of the study.

  • Steelhead Trout were the most numerous fish observed throughout the study, the number of fish observed showed greater variability in the first five eyars of the study and greater stability, though lower numbers, in the second five years.

  • The number of Coho Salmon observed passing through the Willamette Falls fish ladder varied throughout the study with a large increase int he last two years (with a more than five-fold increase between 2008 and 2009).